Trimmomatic is a flexible read trimming tool for Illumina NGS data.

• Version: 0.33
• Added: September, 2015
• Link: http://www.usadellab.org/cms/?page=trimmomatic

See versions of Trimmomatic which are available:

$ module avail trimmomatic

Load and run trimmomatic:

$ module load trimmomatic/0.33
$ trimmomatic

Notes from the sysadmin during installation:

$ cd /tmp/
$ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
$ cd Trimmomatic-0.33
$ sudo mkdir -p /export/apps/trimmomatic/0.33
$ sudo cp -rv . /export/apps/trimmomatic/0.33/

I created a wrapper shell script named trimmomatic to run Trimmomatic, otherwise, you'll have to specify a path to trimmomatic-0.33.jar—java -jar <path to trimmomatic.jar> …—which is unfriendly. /export/apps/trimmomatic/0.33/trimmomatic:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)
java -jar $PREFIX/trimmomatic-0.33.jar $*